RT Journal Article
SR Electronic
T1 Dimensionality reduction by UMAP to visualize physical and genetic interactions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 681726
DO 10.1101/681726
A1 Michael W. Dorrity
A1 Lauren M. Saunders
A1 Christine Queitsch
A1 Stanley Fields
A1 Cole Trapnell
YR 2019
UL http://biorxiv.org/content/early/2019/06/25/681726.abstract
AB Dimensionality reduction is often used to visualize complex expression profiling data. Here, we use the Uniform Manifold Approximation and Projection (UMAP) method on published transcript profiles of 1484 single gene deletions of Saccharomyces cerevisiae. Proximity in low-dimensional UMAP space identifies clusters of genes that correspond to protein complexes and pathways, and finds novel protein interactions even within well-characterized complexes. This approach is more sensitive than previous methods and should be broadly useful as additional transcriptome datasets become available for other organisms.